2ZZV

Crystal Structure of a Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate

Akiyama, N.Takeda, K.Miki, K.

(2009) J Mol Biol 392: 559-565

  • DOI: 10.1016/j.jmb.2009.07.043
  • Primary Citation of Related Structures:  
    2ZZV, 2ZZW, 2ZZX

  • PubMed Abstract: 
  • Lactate is utilized in many biological processes, and its transport across biological membranes is mediated with various types of transporters. Here, we report the crystal structures of a lactate-binding protein of a TRAP (tripartite ATP-independent periplasmic) secondary transporter from Thermus thermophilus HB8 ...

    Lactate is utilized in many biological processes, and its transport across biological membranes is mediated with various types of transporters. Here, we report the crystal structures of a lactate-binding protein of a TRAP (tripartite ATP-independent periplasmic) secondary transporter from Thermus thermophilus HB8. The folding of the protein is typical for a type II periplasmic solute-binding protein and forms a dimer in a back-to-back manner. One molecule of l-lactate is clearly identified in a cleft of the protein as a complex with a calcium ion. Detailed crystallographic and biochemical analyses revealed that the calcium ion can be removed from the protein and replaced with other divalent cations. This characterization of the structure of a protein binding with calcium lactate makes a significant contribution to our understanding of the mechanisms by which calcium and lactate are accommodated in cells.


    Organizational Affiliation

    Department of Chemistry, Kyoto University, Sakyo-ku, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC transporter, solute-binding proteinA, B361Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0766
Find proteins for Q5SK82 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SK82 
Go to UniProtKB:  Q5SK82
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAC
Query on LAC

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.052α = 90
b = 77.335β = 90
c = 136.389γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance